Joint X-ray/neutron structure of Trichoderma reesei xylanase II in complex with MES at pH 5.7
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 6 | 290 | 1.5M MES, 0.2M NaI, PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 6.0 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.5 | 50.84 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 49.174 | α = 90 |
| b = 60.214 | β = 90 |
| c = 70.434 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 21 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 293 | IMAGE PLATE | RIGAKU RAXIS IV++ | OSMIC VARIMAX | 2009-10-10 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 291 | AREA DETECTOR | 3HE POSITION SENSITIVE DETECTOR | | 2010-02-02 | | |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | | |
| 2 | NUCLEAR REACTOR | OTHER | 0.7-6.0 | | PCS |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot |
|---|
| 1 | 1.55 | 40 | 97.9 | 0.046 | | | | | | 22.2 | 4 | | 30402 | | | |
| 2 | 2 | 22.85 | 85.5 | 0.223 | | | | | | 5 | 3.3 | | 12398 | | 1.4 | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.55 | 1.61 | | 0.203 | | | | | | 4.6 | 2.4 | |
| 2 | 2 | 2.11 | | 0.369 | | | | | | 1.6 | 2 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.6 | 19.99 | | | 28247 | 26744 | 1351 | 94.7 | | | 0.192 | 0.17 | 0.196 | 0.19 | RANDOM | 22.77 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 19.99 | | | 14658 | 11689 | 588 | 79.7 | | | 0.243 | | 0.279 | | RANDOM | 22.77 |
| Temperature Factor Modeling |
|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
|---|
| | | | | |
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| x_dihedral_angle_d | 23.5 |
| x_dihedral_angle_d | 23.5 |
| x_improper_angle_d | 2.62 |
| x_improper_angle_d | 2.62 |
| x_angle_deg | 1 |
| x_angle_deg | 1 |
| x_bond_d | 0.01 |
| x_bond_d | 0.01 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1480 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 151 |
| Heterogen Atoms | 13 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| nCNS | refinement |
| HKL-2000 | data collection |
| d*TREK | data scaling |
| HKL-2000 | data reduction |
| d*TREK | data reduction |
| HKL-2000 | data scaling |
| CNS | phasing |
